The tool provides the following output,
- complete_bigy_autosomal.csv - contains all identified SNPs in BigY BAM file.
- complete_bigy_mtdna.fasta - mtDNA found in BigY in FASTA format.
- complete_bigy_x.csv - contains all identified X-DNA SNPs in BigY BAM file.
- complete_bigy_y.csv - contains all identified SNPs in 23andMe format with RSIDs.
- ftdna_bigy_autosomal.csv - contains only SNPs tested by FTDNA that are found in BigY BAM file.
- ftdna_bigy_mtdna.fasta - mtDNA found in BigY in FASTA format (duplicate output - same as complete_bigy_mtdna.fasta).
- ftdna_bigy_x.csv - contains only X-DNA SNPs tested by FTDNA that are found in BigY BAM file.
- ftdna_bigy_y.csv - contains all identified Y-SNPs in FTDNA table format.
- ftdna_bigy_ysnps.txt - contains all identified Y-SNPs separated by comma.
- Windows 64 bit Operating System
- Microsoft .Net Framework 4.0
- 10 GB of free hard disk space.
- Minimum 2 GB RAM.
Extract the download and click 'Big-Y BAM Analysis UI.exe'. Select the .BAM file and click 'Start Analysis'.
After clicking 'Start Analysis', a command prompt will automatically open and start executing series of commands.
After around 4-8 hours (depending on your computer speed), the output will be available inside a subfolder called 'out'. Also ignore any error with file-not-found, esp. on the last completion screen.
Source Code at GitHub.
License: The download bundles the following software for easy usage. So, if you are using this tool for non-commercial and/or personal use, you should be alight.
- BOW (samtools) - GNU GPLv2
- Genome Analysis Tool Kit - Non commercial License.
- Cygwin - GNU GPL v3
- BigY FTDNA VCF - MIT License
- Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]
- McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-303. [Pubmed]
- Forms UI error handling.
- A fail-back console batch file include.
- Source for UI included.
- Reduced the size of download by removing unnecessary files.
- Streamlined everything to be 64-bit.
- Changed the user interface from console to windows forms.
- Optimized to use 90% of available memory in the system.
Change Log :1.0
- Initial Release.